Starting phenix.real_space_refine on Tue Apr 29 03:00:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihj_35446/04_2025/8ihj_35446.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihj_35446/04_2025/8ihj_35446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihj_35446/04_2025/8ihj_35446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihj_35446/04_2025/8ihj_35446.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihj_35446/04_2025/8ihj_35446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihj_35446/04_2025/8ihj_35446.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5450 2.51 5 N 1435 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8509 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2234 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 273} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1702 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1701 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2480 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'P9X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.02, per 1000 atoms: 0.59 Number of scatterers: 8509 At special positions: 0 Unit cell: (93.6, 116.22, 132.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1571 8.00 N 1435 7.00 C 5450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 37.6% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'R' and resid 23 through 28 removed outlier: 3.705A pdb=" N ALA R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 55 removed outlier: 3.513A pdb=" N LEU R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.613A pdb=" N VAL R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 127 removed outlier: 3.515A pdb=" N LEU R 102 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA R 108 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 138 removed outlier: 3.729A pdb=" N ASN R 137 " --> pdb=" O HIS R 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS R 138 " --> pdb=" O ALA R 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 134 through 138' Processing helix chain 'R' and resid 140 through 158 removed outlier: 3.835A pdb=" N VAL R 156 " --> pdb=" O TRP R 152 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY R 157 " --> pdb=" O GLY R 153 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 165 removed outlier: 4.024A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS R 165 " --> pdb=" O HIS R 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 160 through 165' Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.910A pdb=" N PHE R 193 " --> pdb=" O HIS R 189 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.600A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 260 removed outlier: 3.744A pdb=" N ALA R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.590A pdb=" N VAL R 250 " --> pdb=" O PRO R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 280 removed outlier: 4.239A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 294 removed outlier: 3.951A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET R 288 " --> pdb=" O TYR R 284 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.753A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.628A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.149A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.576A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.766A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.769A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.823A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.990A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.619A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.727A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.690A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.833A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.521A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 169 through 171 removed outlier: 3.542A pdb=" N ILE R 169 " --> pdb=" O VAL R 176 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 174 " --> pdb=" O ASN R 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 9.442A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.716A pdb=" N SER S 7 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 58 through 60 Processing sheet with id=AA5, first strand: chain 'S' and resid 45 through 46 removed outlier: 3.502A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.500A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.571A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.516A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.561A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.776A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.979A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.565A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.505A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.062A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2734 1.34 - 1.46: 2178 1.46 - 1.58: 3720 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 8703 Sorted by residual: bond pdb=" C5 P9X R 501 " pdb=" O2 P9X R 501 " ideal model delta sigma weight residual 1.250 1.306 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" C4 P9X R 501 " pdb=" C5 P9X R 501 " ideal model delta sigma weight residual 1.530 1.481 0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" CG PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.69e+00 bond pdb=" CB GLN A 333 " pdb=" CG GLN A 333 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.56e+00 bond pdb=" C5 P9X R 501 " pdb=" O3 P9X R 501 " ideal model delta sigma weight residual 1.248 1.224 0.024 2.00e-02 2.50e+03 1.49e+00 ... (remaining 8698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 11613 1.36 - 2.72: 170 2.72 - 4.08: 33 4.08 - 5.44: 14 5.44 - 6.80: 7 Bond angle restraints: 11837 Sorted by residual: angle pdb=" CA GLN A 333 " pdb=" CB GLN A 333 " pdb=" CG GLN A 333 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 107.55 4.45 1.40e+00 5.10e-01 1.01e+01 angle pdb=" CB GLN A 333 " pdb=" CG GLN A 333 " pdb=" CD GLN A 333 " ideal model delta sigma weight residual 112.60 117.41 -4.81 1.70e+00 3.46e-01 8.00e+00 angle pdb=" CA ASP S 201 " pdb=" C ASP S 201 " pdb=" N ARG S 202 " ideal model delta sigma weight residual 118.59 122.38 -3.79 1.63e+00 3.76e-01 5.40e+00 angle pdb=" C4 P9X R 501 " pdb=" C5 P9X R 501 " pdb=" O3 P9X R 501 " ideal model delta sigma weight residual 116.38 121.98 -5.60 3.00e+00 1.11e-01 3.48e+00 ... (remaining 11832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4401 18.01 - 36.02: 534 36.02 - 54.04: 116 54.04 - 72.05: 24 72.05 - 90.06: 9 Dihedral angle restraints: 5084 sinusoidal: 1832 harmonic: 3252 Sorted by residual: dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " pdb=" OD1 ASP B 195 " ideal model delta sinusoidal sigma weight residual -30.00 -90.12 60.12 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual -86.00 -114.57 28.57 1 1.00e+01 1.00e-02 1.17e+01 ... (remaining 5081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 831 0.027 - 0.054: 317 0.054 - 0.081: 126 0.081 - 0.108: 52 0.108 - 0.135: 32 Chirality restraints: 1358 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE R 178 " pdb=" N ILE R 178 " pdb=" C ILE R 178 " pdb=" CB ILE R 178 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA VAL S 147 " pdb=" N VAL S 147 " pdb=" C VAL S 147 " pdb=" CB VAL S 147 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1355 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO S 75 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 98 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO R 99 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 99 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 99 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO S 236 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.027 5.00e-02 4.00e+02 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 248 2.70 - 3.25: 8082 3.25 - 3.80: 12738 3.80 - 4.35: 16676 4.35 - 4.90: 28903 Nonbonded interactions: 66647 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.193 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.217 3.040 nonbonded pdb=" O ILE S 138 " pdb=" OG1 THR S 238 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASN R 68 " pdb=" OG SER R 148 " model vdw 2.289 3.040 ... (remaining 66642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 8706 Z= 0.103 Angle : 0.475 6.803 11843 Z= 0.248 Chirality : 0.039 0.135 1358 Planarity : 0.005 0.112 1499 Dihedral : 16.684 90.058 2973 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.11 % Allowed : 27.10 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1106 helix: -0.25 (0.28), residues: 350 sheet: -0.09 (0.33), residues: 263 loop : -1.04 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS R 133 PHE 0.018 0.001 PHE R 107 TYR 0.020 0.001 TYR S 235 ARG 0.009 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.28286 ( 372) hydrogen bonds : angle 8.23622 ( 1053) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.68988 ( 6) covalent geometry : bond 0.00225 ( 8703) covalent geometry : angle 0.47462 (11837) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.893 Fit side-chains REVERT: A 271 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7979 (ptmm) REVERT: A 313 ARG cc_start: 0.6520 (mtp180) cc_final: 0.5855 (ptp-170) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.2307 time to fit residues: 37.8932 Evaluate side-chains 117 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.0670 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102749 restraints weight = 11069.108| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.76 r_work: 0.3135 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8706 Z= 0.213 Angle : 0.575 8.952 11843 Z= 0.309 Chirality : 0.044 0.198 1358 Planarity : 0.005 0.071 1499 Dihedral : 5.216 54.165 1221 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.36 % Allowed : 24.11 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1106 helix: 0.56 (0.27), residues: 363 sheet: 0.05 (0.32), residues: 266 loop : -1.27 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.016 0.001 PHE S 27 TYR 0.024 0.001 TYR S 235 ARG 0.004 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.05823 ( 372) hydrogen bonds : angle 5.23943 ( 1053) SS BOND : bond 0.00081 ( 3) SS BOND : angle 0.93357 ( 6) covalent geometry : bond 0.00504 ( 8703) covalent geometry : angle 0.57517 (11837) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.943 Fit side-chains REVERT: S 93 MET cc_start: 0.8002 (ttt) cc_final: 0.7777 (ttt) REVERT: S 235 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.6481 (t80) REVERT: B 234 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8554 (t80) outliers start: 38 outliers final: 18 residues processed: 156 average time/residue: 0.2043 time to fit residues: 43.8744 Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 9.9990 chunk 35 optimal weight: 0.0570 chunk 96 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 overall best weight: 3.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102134 restraints weight = 11206.986| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.79 r_work: 0.3132 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8706 Z= 0.204 Angle : 0.559 9.854 11843 Z= 0.297 Chirality : 0.044 0.210 1358 Planarity : 0.004 0.056 1499 Dihedral : 5.049 48.093 1221 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.59 % Allowed : 24.45 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1106 helix: 0.98 (0.28), residues: 363 sheet: -0.02 (0.32), residues: 260 loop : -1.37 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.001 PHE S 27 TYR 0.025 0.002 TYR S 235 ARG 0.004 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 372) hydrogen bonds : angle 4.81444 ( 1053) SS BOND : bond 0.00045 ( 3) SS BOND : angle 0.93816 ( 6) covalent geometry : bond 0.00488 ( 8703) covalent geometry : angle 0.55844 (11837) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.913 Fit side-chains REVERT: R 277 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.7035 (t80) REVERT: S 93 MET cc_start: 0.7998 (ttt) cc_final: 0.7776 (ttt) REVERT: S 235 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6285 (t80) REVERT: B 234 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8655 (t80) REVERT: C 37 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7897 (tt) outliers start: 40 outliers final: 19 residues processed: 154 average time/residue: 0.2011 time to fit residues: 43.1481 Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 105 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101513 restraints weight = 11111.804| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.77 r_work: 0.3121 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8706 Z= 0.228 Angle : 0.575 10.102 11843 Z= 0.304 Chirality : 0.044 0.212 1358 Planarity : 0.004 0.054 1499 Dihedral : 4.973 48.753 1221 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.43 % Allowed : 23.08 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1106 helix: 0.96 (0.28), residues: 367 sheet: -0.11 (0.31), residues: 265 loop : -1.37 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.018 0.002 PHE S 27 TYR 0.025 0.002 TYR S 235 ARG 0.005 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04812 ( 372) hydrogen bonds : angle 4.71816 ( 1053) SS BOND : bond 0.00106 ( 3) SS BOND : angle 1.04379 ( 6) covalent geometry : bond 0.00549 ( 8703) covalent geometry : angle 0.57446 (11837) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 0.903 Fit side-chains REVERT: R 34 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7421 (tt) REVERT: R 38 PHE cc_start: 0.7819 (t80) cc_final: 0.7599 (t80) REVERT: R 45 ASN cc_start: 0.8007 (m-40) cc_final: 0.7722 (m110) REVERT: R 102 LEU cc_start: 0.7182 (tt) cc_final: 0.6964 (tp) REVERT: R 277 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6975 (t80) REVERT: A 272 ASP cc_start: 0.8135 (m-30) cc_final: 0.7883 (m-30) REVERT: S 93 MET cc_start: 0.8005 (ttt) cc_final: 0.7758 (ttt) REVERT: S 235 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6369 (t80) REVERT: S 237 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7491 (pp) REVERT: B 234 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8662 (t80) outliers start: 56 outliers final: 38 residues processed: 169 average time/residue: 0.1894 time to fit residues: 44.9580 Evaluate side-chains 159 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 53 CYS Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.159996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110238 restraints weight = 10950.489| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.10 r_work: 0.3179 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8706 Z= 0.095 Angle : 0.479 9.820 11843 Z= 0.253 Chirality : 0.041 0.139 1358 Planarity : 0.004 0.051 1499 Dihedral : 4.807 45.668 1221 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.56 % Allowed : 26.18 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1106 helix: 1.36 (0.29), residues: 368 sheet: -0.10 (0.31), residues: 264 loop : -1.19 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.004 0.000 HIS S 35 PHE 0.011 0.001 PHE R 105 TYR 0.019 0.001 TYR S 235 ARG 0.006 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 372) hydrogen bonds : angle 4.34981 ( 1053) SS BOND : bond 0.00491 ( 3) SS BOND : angle 0.86658 ( 6) covalent geometry : bond 0.00203 ( 8703) covalent geometry : angle 0.47920 (11837) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.986 Fit side-chains REVERT: R 45 ASN cc_start: 0.7918 (m-40) cc_final: 0.7541 (m110) REVERT: R 192 MET cc_start: 0.5545 (tmm) cc_final: 0.5201 (tpp) REVERT: R 277 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.7028 (t80) REVERT: A 298 GLU cc_start: 0.7776 (tt0) cc_final: 0.7575 (tt0) REVERT: A 309 ASP cc_start: 0.7758 (t0) cc_final: 0.7534 (t0) REVERT: A 313 ARG cc_start: 0.6715 (mtp180) cc_final: 0.5694 (ptp-170) REVERT: S 93 MET cc_start: 0.7893 (ttt) cc_final: 0.7618 (ttt) REVERT: S 202 ARG cc_start: 0.7614 (mtm-85) cc_final: 0.7369 (mtm-85) REVERT: S 235 TYR cc_start: 0.6352 (OUTLIER) cc_final: 0.5744 (t80) outliers start: 31 outliers final: 21 residues processed: 155 average time/residue: 0.1980 time to fit residues: 42.7009 Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 184 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 32 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106562 restraints weight = 10942.053| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.85 r_work: 0.3190 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8706 Z= 0.108 Angle : 0.490 10.836 11843 Z= 0.256 Chirality : 0.041 0.142 1358 Planarity : 0.004 0.055 1499 Dihedral : 4.400 39.041 1221 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.67 % Allowed : 26.64 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1106 helix: 1.44 (0.28), residues: 369 sheet: -0.04 (0.31), residues: 261 loop : -1.11 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.000 HIS S 35 PHE 0.022 0.001 PHE R 276 TYR 0.017 0.001 TYR S 235 ARG 0.007 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 372) hydrogen bonds : angle 4.21833 ( 1053) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.86384 ( 6) covalent geometry : bond 0.00243 ( 8703) covalent geometry : angle 0.48928 (11837) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.253 Fit side-chains REVERT: R 45 ASN cc_start: 0.7902 (m-40) cc_final: 0.7629 (m110) REVERT: R 192 MET cc_start: 0.5655 (tmm) cc_final: 0.5253 (tpp) REVERT: R 277 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6969 (t80) REVERT: A 298 GLU cc_start: 0.7784 (tt0) cc_final: 0.7580 (tt0) REVERT: A 309 ASP cc_start: 0.7817 (t0) cc_final: 0.7560 (t0) REVERT: A 313 ARG cc_start: 0.6685 (mpp-170) cc_final: 0.5763 (ptp-170) REVERT: S 93 MET cc_start: 0.7912 (ttt) cc_final: 0.7652 (ttt) REVERT: S 202 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7325 (mtm-85) REVERT: S 235 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.5942 (t80) outliers start: 32 outliers final: 23 residues processed: 156 average time/residue: 0.2187 time to fit residues: 47.3060 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 ASN B 32 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102379 restraints weight = 11099.434| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.78 r_work: 0.3129 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8706 Z= 0.213 Angle : 0.565 11.874 11843 Z= 0.297 Chirality : 0.044 0.196 1358 Planarity : 0.004 0.053 1499 Dihedral : 4.837 47.233 1221 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.28 % Allowed : 25.95 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1106 helix: 1.26 (0.28), residues: 371 sheet: -0.05 (0.31), residues: 265 loop : -1.28 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.018 0.002 PHE S 27 TYR 0.023 0.001 TYR S 235 ARG 0.007 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 372) hydrogen bonds : angle 4.40563 ( 1053) SS BOND : bond 0.00096 ( 3) SS BOND : angle 0.93069 ( 6) covalent geometry : bond 0.00516 ( 8703) covalent geometry : angle 0.56434 (11837) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 120 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: R 45 ASN cc_start: 0.7956 (m-40) cc_final: 0.7739 (m110) REVERT: R 192 MET cc_start: 0.5856 (tmm) cc_final: 0.5393 (tpp) REVERT: R 277 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6944 (t80) REVERT: A 309 ASP cc_start: 0.7854 (t0) cc_final: 0.7587 (t0) REVERT: S 93 MET cc_start: 0.7987 (ttt) cc_final: 0.7714 (ttt) REVERT: S 235 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.6275 (t80) REVERT: S 237 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7441 (pp) outliers start: 46 outliers final: 34 residues processed: 159 average time/residue: 0.2200 time to fit residues: 47.4447 Evaluate side-chains 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 53 CYS Chi-restraints excluded: chain R residue 59 TRP Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 0.0670 chunk 23 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 32 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.159257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.106449 restraints weight = 11173.849| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.80 r_work: 0.3190 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8706 Z= 0.106 Angle : 0.492 11.214 11843 Z= 0.258 Chirality : 0.041 0.145 1358 Planarity : 0.004 0.051 1499 Dihedral : 4.446 41.455 1221 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.67 % Allowed : 27.32 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1106 helix: 1.48 (0.28), residues: 370 sheet: 0.04 (0.32), residues: 256 loop : -1.16 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.018 0.001 PHE R 276 TYR 0.019 0.001 TYR S 235 ARG 0.008 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 372) hydrogen bonds : angle 4.20502 ( 1053) SS BOND : bond 0.00100 ( 3) SS BOND : angle 0.90509 ( 6) covalent geometry : bond 0.00237 ( 8703) covalent geometry : angle 0.49145 (11837) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 2.662 Fit side-chains revert: symmetry clash REVERT: R 37 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7117 (mm-30) REVERT: R 45 ASN cc_start: 0.7855 (m-40) cc_final: 0.7642 (m110) REVERT: R 192 MET cc_start: 0.5896 (tmm) cc_final: 0.5393 (tpp) REVERT: R 277 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6954 (t80) REVERT: A 298 GLU cc_start: 0.7802 (tt0) cc_final: 0.7597 (tt0) REVERT: A 309 ASP cc_start: 0.7856 (t0) cc_final: 0.7577 (t0) REVERT: S 93 MET cc_start: 0.7923 (ttt) cc_final: 0.7685 (ttt) REVERT: S 202 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7174 (ptt90) REVERT: S 235 TYR cc_start: 0.6346 (OUTLIER) cc_final: 0.5935 (t80) REVERT: S 237 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7020 (pp) outliers start: 32 outliers final: 26 residues processed: 152 average time/residue: 0.2469 time to fit residues: 53.7200 Evaluate side-chains 148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 62 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.161755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108926 restraints weight = 11072.176| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.89 r_work: 0.3226 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8706 Z= 0.093 Angle : 0.465 10.003 11843 Z= 0.246 Chirality : 0.040 0.131 1358 Planarity : 0.004 0.054 1499 Dihedral : 4.182 35.202 1221 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.33 % Allowed : 27.55 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1106 helix: 1.61 (0.28), residues: 371 sheet: 0.17 (0.32), residues: 248 loop : -1.08 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.000 HIS S 35 PHE 0.010 0.001 PHE R 107 TYR 0.015 0.001 TYR S 235 ARG 0.008 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 372) hydrogen bonds : angle 4.03942 ( 1053) SS BOND : bond 0.00104 ( 3) SS BOND : angle 0.87657 ( 6) covalent geometry : bond 0.00205 ( 8703) covalent geometry : angle 0.46507 (11837) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: R 45 ASN cc_start: 0.7819 (m-40) cc_final: 0.7532 (m110) REVERT: R 192 MET cc_start: 0.5805 (tmm) cc_final: 0.5315 (tpp) REVERT: R 277 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.7039 (t80) REVERT: A 309 ASP cc_start: 0.7898 (t0) cc_final: 0.7601 (t0) REVERT: S 93 MET cc_start: 0.7942 (ttt) cc_final: 0.7663 (ttt) REVERT: S 202 ARG cc_start: 0.7570 (mtm-85) cc_final: 0.7092 (ptt90) REVERT: S 235 TYR cc_start: 0.6141 (OUTLIER) cc_final: 0.5879 (t80) REVERT: S 237 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6732 (pp) outliers start: 29 outliers final: 21 residues processed: 147 average time/residue: 0.2077 time to fit residues: 41.9537 Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.163816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113750 restraints weight = 10874.195| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.35 r_work: 0.3225 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8706 Z= 0.089 Angle : 0.458 9.989 11843 Z= 0.241 Chirality : 0.040 0.132 1358 Planarity : 0.004 0.053 1499 Dihedral : 4.040 33.678 1221 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.87 % Allowed : 28.70 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1106 helix: 1.72 (0.28), residues: 371 sheet: 0.22 (0.32), residues: 247 loop : -1.07 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.000 HIS S 35 PHE 0.008 0.001 PHE S 27 TYR 0.014 0.001 TYR S 235 ARG 0.008 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 372) hydrogen bonds : angle 3.98315 ( 1053) SS BOND : bond 0.00142 ( 3) SS BOND : angle 0.87600 ( 6) covalent geometry : bond 0.00193 ( 8703) covalent geometry : angle 0.45799 (11837) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: R 37 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7065 (mm-30) REVERT: R 45 ASN cc_start: 0.7803 (m-40) cc_final: 0.7588 (m110) REVERT: R 192 MET cc_start: 0.5741 (tmm) cc_final: 0.5267 (tpp) REVERT: R 259 HIS cc_start: 0.7872 (t70) cc_final: 0.7437 (t70) REVERT: R 277 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.7124 (t80) REVERT: A 271 LYS cc_start: 0.8065 (ptmt) cc_final: 0.7772 (ptmm) REVERT: A 309 ASP cc_start: 0.7930 (t0) cc_final: 0.7647 (t0) REVERT: S 93 MET cc_start: 0.7940 (ttt) cc_final: 0.7639 (ttt) REVERT: S 202 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7038 (ptt90) REVERT: S 237 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6622 (pp) outliers start: 25 outliers final: 22 residues processed: 146 average time/residue: 0.2253 time to fit residues: 44.8753 Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 53 CYS Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 285 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 56 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 32 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.161628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109642 restraints weight = 11038.323| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.81 r_work: 0.3236 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8706 Z= 0.097 Angle : 0.466 9.971 11843 Z= 0.245 Chirality : 0.041 0.135 1358 Planarity : 0.004 0.049 1499 Dihedral : 4.081 33.045 1221 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.33 % Allowed : 28.01 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1106 helix: 1.74 (0.28), residues: 371 sheet: 0.13 (0.32), residues: 258 loop : -1.11 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.000 HIS S 35 PHE 0.010 0.001 PHE S 27 TYR 0.019 0.001 TYR S 235 ARG 0.009 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 372) hydrogen bonds : angle 3.97406 ( 1053) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.88443 ( 6) covalent geometry : bond 0.00218 ( 8703) covalent geometry : angle 0.46591 (11837) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5420.13 seconds wall clock time: 95 minutes 32.78 seconds (5732.78 seconds total)